Methods and implementation of a central biosample and data management in a three-centre clinical study

Angelow, Aniela; Schmidt, Matthias; Weitmann, Kerstin; Schwedler, Susanne; Vogt, Hannes; Havemann, Christoph; Hoffmann, Wolfgang

doi:10.1016/j.cmpb.2008.02.002

Cited by 16 publications

(14 citation statements)

References 14 publications

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“…In the last few years, many of these limits have been overcome by the introduction of electronic medical records (EMR), which may simplify the data collection and allow more appropriate and timely approaches [1][2][3].…”

Section: Introductionmentioning

confidence: 99%

A prospective survey of febrile events in hematological malignancies

et al. 2011

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The Hema e-Chart prospectively collected data on febrile events (FEs) in hematological malignancy patients (HMs). The aim of the study was to assess the number, causes and outcome of HM-related FEs. Data were collected in a computerized registry that systematically approached the study and the evolution of FEs developing in a cohort of adult HMs who were admitted to 19 hematology departments in Italy from March 2007 to December 2008. A total of 869 FEs in 3,197 patients with newly diagnosed HMs were recorded. Fever of unidentified origin (FUO) was observed in 386 cases (44.4%). The other causes of FE were identified as noninfectious in 48 cases (5.5%) and infectious in 435 cases (50.1%). Bacteria were the most common cause of infectious FEs (301 cases), followed by fungi (95 cases), and viruses (7 cases). Mixed agents were isolated in 32 episodes. The attributable mortality rate was 6.7% (58 FEs). No deaths were observed in viral infection or in the noninfectious groups, while 25 deaths were due to FUO, 16 to bacterial infections, 14 to fungal infections, and three to mixed infections. The Hema e-Chart provided a complete system for the epidemiological study of infectious complications in HMs.

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Section: Introductionmentioning

confidence: 99%

A prospective survey of febrile events in hematological malignancies

et al. 2011

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“…The scope of a genebank may be extended to that of a DNA bank, similar to biobanks devoted to target medical research [159]. The various implications of DNA banks for PGR have been discussed elsewhere.…”

Section: Discussionmentioning

confidence: 99%

NGS technologies for analyzing germplasm diversity in genebanks*

Kilian

Graner²

2012

Briefings in Functional Genomics

137

110

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More than 70 years after the first ex situ genebanks have been established, major efforts in this field are still concerned with issues related to further completion of individual collections and securing of their storage. Attempts regarding valorization of ex situ collections for plant breeders have been hampered by the limited availability of phenotypic and genotypic information. With the advent of molecular marker technologies first efforts were made to fingerprint genebank accessions, albeit on a very small scale and mostly based on inadequate DNA marker systems. Advances in DNA sequencing technology and the development of high-throughput systems for multiparallel interrogation of thousands of single nucleotide polymorphisms (SNPs) now provide a suite of technological platforms facilitating the analysis of several hundred of Gigabases per day using state-of-the-art sequencing technology or, at the same time, of thousands of SNPs. The present review summarizes recent developments regarding the deployment of these technologies for the analysis of plant genetic resources, in order to identify patterns of genetic diversity, map quantitative traits and mine novel alleles from the vast amount of genetic resources maintained in genebanks around the world. It also refers to the various shortcomings and bottlenecks that need to be overcome to leverage the full potential of high-throughput DNA analysis for the targeted utilization of plant genetic resources.

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“…[13][14][15]). Nevertheless, IT support is still limited and restricted to proprietary self-developed biorepository management solutions.…”

Section: Discussionmentioning

confidence: 99%

“…Nevertheless, existing publications are mostly limited to either high level descriptions of the database and communication structure as well as the biobank's data safety concept [14] or very technical implementation details [15]. The latter publication nicely illustrates how the different components of the information processing infrastructure support processes and workflows between the partners, such as sampling, labelling, sample documentation, freezer capacity management and quality control for a three centre clinical study in Greifswald and Berlin.…”

Section: Introductionmentioning

confidence: 99%

“…The collection and storage of tissue samples within hospital-based comprehensive cancer centers (mostly initiated and managed by pathology departments) [13], the creation of large biobanks in multicenter research networks [14,15] and small monocentric collections within specific clinical trials are just examples of this development. Even though literature shows that much progress has already been made in these areas, it has been stated that the specific development of information systems, especially to support biobanking activities, still is a rate-limiting challenge for even faster high quality translational research [16].…”

Section: Introductionmentioning

confidence: 99%

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IT Infrastructure Components for Biobanking

Prokosch

Beck²,

Ganslandt³

et al. 2010

Appl Clin Inform

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KeywordsRequirement specification, biobanking, translational research information technology infrastructure SummaryObjective: Within translational research projects in the recent years large biobanks have been established, mostly supported by homegrown, proprietary software solutions. No general requirements for biobanking IT infrastructures have been published yet. This paper presents an exemplary biobanking IT architecture, a requirements specification for a biorepository management tool and exemplary illustrations of three major types of requirements. Methods: We have pursued a comprehensive literature review for biobanking IT solutions and established an interdisciplinary expert panel for creating the requirements specification. The exemplary illustrations were derived from a requirements analysis within two university hospitals. Results: The requirements specification comprises a catalog with more than 130 detailed requirements grouped into 3 major categories and 20 subcategories. Special attention is given to multitenancy capabilities in order to support the project-specific definition of varying research and biobanking contexts, the definition of workflows to track sample processing, sample transportation and sample storage and the automated integration of preanalytic handling and storage robots. Conclusion: IT support for biobanking projects can be based on a federated architectural framework comprising primary data sources for clinical annotations, a pseudonymization service, a clinical data warehouse with a flexible and user-friendly query interface and a biorepository management system. Flexibility and scalability of all such components are vital since large medical facilities such as university hospitals will have to support biobanking for varying monocentric and multicentric research scenarios and multiple medical clients.

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Methods and implementation of a central biosample and data management in a three-centre clinical study

Cited by 16 publications

References 14 publications

A prospective survey of febrile events in hematological malignancies

A prospective survey of febrile events in hematological malignancies

NGS technologies for analyzing germplasm diversity in genebanks*

IT Infrastructure Components for Biobanking

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